Other sites

prettyR

I have just remembered a package called ‘prettyR’ that pretty much does what it says. It makes R code more readable.. so an example from my forthcoming genomeplot package (see forthcoming blog entry):

## this function integrates 3 steps to creating a genome plot## 1 query bioMart to get a GFF like data-frame from ensembl## 2 add new elements to the gff to make it plot with ggplot2## 3 plot it with ggplot2## the reason to split it like this is so that basic users may use this simple function## and advanced users can try custom queries or altered plotting themes with the sep functions
gnmplot= function(filters='hgnc', values='MAF', species='human'){require(biomaRt);require(ggplot2)
gff= getGFF(filters=filters, values=values, species=species)
gff_new=alterGFF()
gnmplot=gffplot(gffnew)return(gnmplot)}

which I think you will agree.. is quite nice. So in future I’ll be using this for all R-code on the website.